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GCP TL-I Phase II WORK PLAN
for Objective 4- chickpea
GCP
ICRISAT, India- Rajeev Varshney, Pooran Gaur, HC Sharma, L Krishnamurthy, Nalini Mallikarjuna, Mahendar Thudi, Siva K. Chamarthi
ICRISAT, Kenya- NVPR Ganga Rao, Said N. Silim
Egerton University, Kenya - Paul Kimurto, Richard Mulwa
Ethiopian Institute of Agricultural Research (EIAR), Ethiopia- Asnake Fikre
Indian Institute of Pulse Research (IIPR) Kanpur, India- Sushil K Chaturvedi, SD Mahapatra,Aditya Pratap
University of California-Davis, USA- Doug Cook, Ming Cheng Luo
DArT Pty Ltd., Yaramulla, Australia- Andrzej Killian
Collaborating Scientists and Institutions
GCP
Genotyping
Introgression
Phenotyping
India, Kenya
& E
thiopia
2007
Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7
SNPs
MA
RS
MA
BC
X
Trait mapping Trait mapping
Reference collection
Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers
Enriched libraries
BAC end sequences
Interspecific population
Intraspecific population Elite lines
25-50 contrast lines
DArTs
SSRs
Genetic maps
Minor effect QTLs
Major effect QTLs
BC3F2
F3
Phase I Har
ness
ing
Diver
sity
Geno
mic
reso
urce
s
Biot
ic s
tres
s re
sist
ance
Abi
otic s
tres
s re
sist
ance
Molec
ular
br
eeding
Capa
city
Building
Dat
a man
agem
net
GCP
Harnessing diversity
Activity 1
Characterization of diversity - extensive phenotyping
MAGIC population Pre-breeding population
GCP
Genotyping
Introgression
Phenotyping
India, Kenya
& E
thiopia
2007
Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7
SNPs
MA
RS
MA
BC
X
Trait mapping Trait mapping
Reference collection
Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers
Enriched libraries
BAC end sequences
Interspecific population
Intraspecific population Elite lines
25-50 contrast lines
DArTs
SSRs
Genetic maps
Minor effect QTLs
Major effect QTLs
BC3F2
F3
Phase I
phenotyping
phenotyping
Pre- breed. populations
MAGIC populations
Subset of MAGIC lines
SUPERIOR LINES
2014
2010
Phase II
Phenotypic data, Markergenotyping data
Dat
a m
anag
emen
t (G
CP
cent
ral r
egis
try &
IC
GG
C)
GCP
Scheme for MAGIC populations
Cavanagh et al. 2008
Parental line Remarks
ICC 4958 Drought-tolerant genotype found to be promising in Ethiopia, Kenya and India; drought-tolerant parent of two mapping populations
ICCV 10 Widely adapted drought-tolerant cultivar found to be promising in India and Kenya
JAKI 9218 Farmer-preferred cultivar in central and southern India
JG 11 Farmer-preferred cultivar in southern India and also performing well in Kenya
JG 130 Farmer-preferred cultivars from central India
JG 16 Farmer-preferred cultivar in northern and central India
ICCV 97105 Farmer-preferred elite line identified in Kenya and Tanzania
ICCV 00108 Farmer-preferred elite line identified in Tanzania
GCP
Timeline for development of MAGIC population
Activity Timeline
Make 28 one-way crosses Oct 2009–Feb 2010
Confirm hybrids by genotyping and make 14 four-way crosses
Mar 2010–Jun 2010
Confirm hybrids by genotyping and make 7 eight-way crosses
Jun 2010–Sep 2010
Grow F1s Oct 2011–Feb 2011
Grow F2 (n=500 minimum) Mar 2011– Jun 2011
Grow F4 (SSD) Jun 2011–Sep 2011
Grow F5 (SSD) Oct 2011– Feb 2012
Grow F6 (SSD) Mar 2012–Jun 2012
Grow F7 (SSD) Jun 2012– Sep 2012
Grow F8 progenies for seed bulking Oct 2012– Feb 2013
Genotyping of selected MAGIC populations Jan 2013–June 2013
Selection of subset of MAGIC lines based on SNP genotyping/haplotype data
June 2013- Sept 2013
• MAGIC lines with enhanced drought tolerance • Fine resolution mapping population
GCP
LG 1
Total marker loci - 1821 Inter-marker distance- 2.48cM
LG 4 LG 3 LG 5 LG 2
LG 6 LG 7
LG 8
Activity 2 in TLI Large scale markers and high-density genetic map
GCP
High-throughput & cost-effective marker genotyping
Integrated with Molecular Breeding Platform for facilitating molecular breeding in high-throughput and cost-effective manner e.g. - genotyping of MAGIC population - genotyping of AB- population - genotyping of MABC population - genotyping of MARS population
GCP
TAA170
GA24
STMS11
ICCM0249
CaM0856
Linkage group 5 harboring hot spot for drought related QTLs in TL-I (Act 4) - 4 markers
Diagnostic markers for accelerating molecular breeding
Genetic map
Physical map
BACs
Candidate QTLs
Additional markers
Marker needs to be Polymorphic in D x R - 30 genotypes tested - 50% success
GCP
Genotyping
Introgression
Phenotyping
India, Kenya
& E
thiopia
2007
Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7
SNPs
MA
RS
MA
BC
X
Trait mapping Trait mapping
Reference collection
Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers
Enriched libraries
BAC end sequences
Interspecific population
Intraspecific population Elite lines
25-50 contrast lines
DArTs
SSRs
Genetic maps
Minor effect QTLs
Major effect QTLs
BC3F2
F3
Phase I
phenotyping
SUPERIOR LINES 2014
2010
Phase II
Phenotypic data, Marker/ BAC end sequences
Dat
a m
anag
emen
t (G
CP
cent
ral r
egis
try &
IC
GG
C)
phenotyping
Pre- breed. populations
MAGIC populations
Subset of MAGIC lines
NG
S
sequencing
SSR markers
SNP resources & genotyping platform
High density genetic maps
BAC contigs
GCP
Phase I- Activity: Marker discovery for insect resistance Natural field conditions Detached leaf assay
- No natural variation in cultivated germplasm - QTL discovery based on interspecific mapping population didn’t yield appropriate QTLs
GCP
JG11 × PI 489777 Nov 2010 - Mar 2011 (Cultivated) (Wild)
F1 Jun 2011 - Oct 2011
BC1F1 Nov 2011 - Mar 2012
BC2F1 Jun 2012 – Oct 2012
BC2F2 (Genotyping) Nov 2012 - Mar 2013
BC2F2:3 (Phenotyping) Jun 2013 – Oct 2013
Identification and charecterisation of ABCLs Nov 2013 - Mar 2013
JG 11 ×
JG 11 ×
×
× QTL Analysis
Scheme for AB-QTL approach
GCP
Genotyping
Introgression
Phenotyping
India, Kenya
& E
thiopia
2007
Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7
SNPs
MA
RS
MA
BC
X
Trait mapping Trait mapping
Reference collection
Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers
Enriched libraries
BAC end sequences
Interspecific population
Intraspecific population Elite lines
25-50 contrast lines
DArTs
SSRs
Genetic maps
Minor effect QTLs
Major effect QTLs
BC3F2
F3
Phase I
JG 11 × PI 489777
AB
-QTL app
AB-QTLs
ABCLs Validation of Q
TLs
SUPERIOR LINES 2014
2010
Phase II
Phenotypic data, Marker/ BAC end sequences, QTLs, QTLs-associated markers
Dat
a m
anag
emen
t (G
CP
cent
ral r
egis
try &
IC
GG
C)
phenotyping
phenotyping
Pre- breed. populations
MAGIC populations
Subset of MAGIC lines
NG
S
sequencing
SSR markers
SNP resources & genotyping platform
High density genetic maps
BAC contigs
Expectations - Candidate markers and QTLs - ABCLs with enhanced resistance to insect resistance - Validation of insect resistance QTL
GCP
- Root traits - Yield - Harvest index - CID - OID
- 2000 cylinder (1.2 m long, 20 cm dm)
Phase I- Activity 4: Large scale drought phenotyping
WUE/ TE phenotyping needs to be undertaken
GCP
Genotyping
Introgression
Phenotyping
India, Kenya
& E
thiopia
2007
Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7
SNPs
MA
RS
MA
BC
X
Trait mapping Trait mapping
Reference collection
Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers
Enriched libraries
BAC end sequences
Interspecific population
Intraspecific population Elite lines
25-50 contrast lines
DArTs
SSRs
Genetic maps
Minor effect QTLs
Major effect QTLs
BC3F2
F3
Phase I
Phenotyping
WU
E, TE
Identification of superior lines for drought tolerance
SUPERIOR LINES 2014
2010
Phase II
Phenotypic data, Marker/ BAC end sequences, QTLs, QTLs-associated markers
Dat
a m
anag
emen
t (G
CP
cent
ral r
egis
try &
IC
GG
C)
phenotyping
phenotyping
Pre- breed. populations
MAGIC populations
Subset of MAGIC lines
JG 11 × PI 489777
AB
-QTL app
AB-QTLs
ABCLs Validation of Q
TLs
NG
S
sequencing
SSR markers
SNP resources & genotyping platform
High density genetic maps
BAC contigs
GCP Expected outputs
1. TE phenotyping reference collection and ICC 4958 × ICC 1882 mapping population
2. Metadata analysis on all set of phenotyping data- best phenotyping methodology
3. Superior lines with enhanced drought tolerance
4. Validation of drought QTL in elite chickpea lines
GCP Crosses: 3 Cultivars x 2 Donors for root traits
BC1: Cultivar x F1 ↓
BC1F1
BC 2: Cultivar x BC1F1 ↓
BC2F1 Subjected to foreground and background selection
BC3: Cultivar x BC2F1 As in BC 2
↓ BC3F1
Selected heterozygous plants for QTL-linked markers and over 90% genome of the recurrent parent
↓ BC3F2
2009-2010 Select homozygous plants for QTL-linked markers ↓
BC3F3 Seed multiplication
↓ Multilocation evaluation BC3F4 lines
TL-I Activity 6 MABC for drought tolerance
Donors
Cultivars
JG 11
Chefe KAK 2
GCP
ICCV 97105: Farmer-preferred desi chickpea elite line identified in Kenya and Tanzania through farmer-participatory varietal selection (FPVS) trials conducted in phase I of TLII. This is being proposed for release in Kenya and Tanzania.
Ejere: Farmer-preferred kabuli chickpea cultivar identified in Ethiopia through FPVS trials conducted in phase I of TLII.
DCP-92-3: Most-popular desi chickpea cultivar in north-eastern India
ICC 4958: Well known drought-tolerant genotype with deep and vigorous root system. It is a drought tolerant parent of two mapping populations for root traits. It has also performed well in Ethiopia, Kenya and India
MABC for drought tolerance by NARS partners Selection of cultivars
GCP Egerton University, Njoro, Kenya
DZARC–Debre Ziet, Ethiopia
IIPR, Kanpur, India
ICCV 97105 × ICC 4958
Ejere × ICC 4958 DCP 92-3 × ICC 4958
Make cross Oct 2009–Mar 2010
Oct 2009–Mar 2010
Nov 2009 – Mar 2010
Grow F1 and make BC1 Apr 2010–Aug 10 Apr 2010–Aug
2010 Jun 2010–Oct 2010
Grow BC1F1, foreground and background selection, make BC2
Oct 2010–Mar 2011
Oct 2010–Mar 2011
Nov 2010–Mar 2011
Grow BC2F1, foreground and background selection, make BC3
Apr 2011–Aug 11 Apr 2011–Aug 2011
Jun 2011–Oct 2011
Grow BC3F1, foreground and background selection, self selected plants
Oct 2011–Mar 12 Oct 2011–Mar 2012
Nov 2011–Mar 2012
Grow BC3F2, select homozygous plants for QTL-linked markers, self selected plants
Apr 2012–Aug 2012
Apr 2012– Aug 2012
Jun 2012–Oct 2012
Grow BC3F3 progenies for seed multiplication
Oct 2012–Mar 2013
Oct 2012–Mar 2013
Nov 2012–Mar 2013
Multilocation evaluation of BC3F4 progenies
Apr 2013 –Aug 2013
Apr 2013–Aug 2013
Nov 2013–Mar 2014
MABC by NARS partners
GCP
Set 1 (2 crosses) Set-2 (3 crosses)
2008/09 Genotyping of F3 plants F2 grown
F4 (Seed mutiplication) Genotyping of F3 plants Multilocation evaluation F4 (Seed mutiplication) of F5 progenies and QTL analysis
Selection and inter-crossing Multilocation evaluation of F3s of F5 progenies and 2009/10 QTL analysis
Five good-by-good crosses involving cultivars from Africa and Asia
TL-I Activity 6 MARS for drought tolerance
GCP
Popu
lation
dev
elop
men
t Re
combi
nation
Popu
lation
de
velopm
ent
1st Recombination cycle 2nd Recombination cycle 3rd Recombination cycle
Multilocation phenotyping
Genotyping
Parent 1 × Parent 2 F1 F2 F3 F3:4 F3:5
Single seed descent 282 F3 progenies 282 progenies
Multilocation phenotyping A B C D E F G H
F1 F1 F1 F1 F1 F1
F1 F2 F3 F3:4
10 plants/family (A-H), 6 sets of 8 families/cross QTL detection
Development of MARS populations continued
GCP
Genotyping
Introgression
Phenotyping
India, Kenya
& E
thiopia
2007
Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7
SNPs
MA
RS
MA
BC
X
Trait mapping Trait mapping
Reference collection
Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers
Enriched libraries
BAC end sequences
Interspecific population
Intraspecific population Elite lines
25-50 contrast lines
DArTs
SSRs
Genetic maps
Minor effect QTLs
Major effect QTLs
BC3F2
F3
Phase I
phenotyping
SUPERIOR LINES 2014
2010
Phase II
Phenotypic data, Marker/ BAC end sequences, QTLs, QTLs-associated markers, Next generation breeders trained
Dat
a m
anag
emen
t (G
CP
cent
ral r
egis
try &
IC
GG
C)
phenotyping
Pre- breed. populations
MAGIC populations
Subset of MAGIC lines
NG
S
sequencing
SSR markers
SNP resources & genotyping platform
High density genetic maps
BAC contigs
JG 11 × PI 489777
AB
-QTL app
AB-QTLs
ABCLs Validation of Q
TLs
Phenotyping
WU
E, TE
Selection of phenotyping
methodology(ies)
BC3F4
BC3F2
MA
BC
(N
AR
S)
Multilocation
phenotyping
F5
Multilocation
phenotyping
Recom
bination cycles
Multilocation
phenotyping
Molecular Breeding Platform
GCP
Genotyping MBP
MBP Phenotyping
New Activity- trait package
Development of populations
- Act 5.2 of TL II
Markers for FW resistance
CMBN Govt of India
Marker screening for root trait QTL and FW resistance associated markers
(TL I)
GCP
Sub-activities:
Strengthening infrastructure in collaboration with Activity 3 of Objective 5
Organization of a modern breeding workshop for TL-I & TL-II breeders of chickpea
Six MSc and three PhD students trained in chickpea genomics and breeding activities
Activity 6: Capacity-building
GCP
Genotyping
Introgression
Phenotyping
India, Kenya
& E
thiopia
2007
Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7
SNPs
MA
RS
MA
BC
X
Trait mapping Trait mapping
Reference collection
Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers
Enriched libraries
BAC end sequences
Interspecific population
Intraspecific population Elite lines
25-50 contrast lines
DArTs
SSRs
Genetic maps
Minor effect QTLs
Major effect QTLs
BC3F2
F3
Phase I
PhD
studentship
Strengthening
Infrastructure
phenotyping
SUPERIOR LINES 2014
2010
Phase II
Phenotypic data, Marker/ BAC end sequences, QTLs, QTLs-associated markers, Next generation breeders trained
Dat
a m
anag
emen
t (G
CP
cent
ral r
egis
try &
IC
GG
C)
phenotyping
Pre- breed. populations
MAGIC populations
Subset of MAGIC lines
NG
S
sequencing
SSR markers
SNP resources & genotyping platform
High density genetic maps
BAC contigs
JG 11 × PI 489777
AB
-QTL app
AB-QTLs
ABCLs Validation of Q
TLs
Phenotyping
WU
E, TE
Selection of phenotyping
methodology(ies)
BC3F4
BC3F2
MA
BC
(N
AR
S)
Multilocation
phenotyping
F5
Multilocation
phenotyping
Recom
bination cycles
Multilocation
phenotyping
GCP
Molecular Breeding Platform
Databases within ICRISAT (Activity 2/ Obj 5)
GCP Central Registry
International Chickpea Genetics & Genomics Consortium (ICGGC)
Data storage & Management
GCP
Genotyping
Introgression
Phenotyping
India, Kenya
& E
thiopia
2007
Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7
SNPs
MA
RS
MA
BC
X
Trait mapping Trait mapping
Reference collection
Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers
Enriched libraries
BAC end sequences
Interspecific population
Intraspecific population Elite lines
25-50 contrast lines
DArTs
SSRs
Genetic maps
Minor effect QTLs
Major effect QTLs
BC3F2
F3
Phase I
phenotyping
SUPERIOR LINES 2014
2010
Phase II
Phenotypic data, Marker/ BAC end sequences, QTLs, QTLs-associated markers, Next generation breeders trained
Dat
a m
anag
emen
t (G
CP
cent
ral r
egis
try &
IC
GG
C)
phenotyping
Pre- breed. populations
MAGIC populations
Subset of MAGIC lines
NG
S
sequencing
SSR markers
SNP resources & genotyping platform
High density genetic maps
BAC contigs
JG 11 × PI 489777
AB
-QTL app
AB-QTLs
ABCLs Validation of Q
TLs
Phenotyping
WU
E, TE
Selection of phenotyping
methodology(ies)
BC3F4
BC3F2
MA
BC
(N
AR
S)
Multilocation
phenotyping
F5
Multilocation
phenotyping
Recom
bination cycles
Multilocation
phenotyping
PhD
studentship
Strengthening
Infrastructure
GCP In summary…
Phase II proposal is based on achievements of Phase I of TLI and requirements of TL II and heavily interacted with Mol Breed Platform
All activities are downstream application oriented
Flexible- open for more suggestions from TL II
Diagnostic markers for drought and insect res.
Superior lines (MAGIC, ABCLs, MABCs, MARS) for drought tolerance and insect resistance
Mol breeding being undertaken by NARS
GCP